[AMBER] Analysis of REMD trajectories (YM)

From: Yip Yew Mun <yipy0005.gmail.com>
Date: Wed, 20 Nov 2013 15:45:34 +0800


I have read an article entitled “Molecular Dynamics Simulations of Protein Folding” by Angel E. Garcia, it’s a Springer article. Inside the article, the author plotted 2 graphs: 1) < E > against T, 2) 𝜎 against T in order to ascertain whether the chosen temperature range and exchange probability work fine. I wish to do the same to my REMD simulations, how can I do it with AMBER?

If unable, is there other ways I can check if the temperature range and exchange probability that I chosen are working fine?


Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University

AMBER mailing list
Received on Wed Nov 20 2013 - 00:00:03 PST
Custom Search